def setUp(self):
# Defaults
self.verbose = False
self.mode = "dir"
self.tracks = {"vertebrate": "chr1.phyloP44way.vertebrate.short.wigFix",
"placental": "chr1.phyloP44way.placental.short.wigFix",
"primate": "chr1.phyloP44way.primate.short.wigFix"}
# Track to be added by test_add_track
self.new_track = ("dnase", "chr1.wgEncodeDukeDNaseSeqBase"
"OverlapSignalK562V2.wig")
# Potentially override defaults
self.init() # Call to sub-classed method
# Create Genomedata collection from test files
seqs = ["chr1.short.fa", "chrY.short.fa.gz"]
# Placental includes data for chr1 and chrY
if self.mode == "dir":
gdfilename = make_temp_dir()
elif self.mode == "file":
tempfile, gdfilename = mkstemp(prefix="genomedata")
os.close(tempfile)
os.remove(gdfilename) # Allow load_genomedata to create it
else:
self.fail("Unrecognized mode: %s" % self.mode)
self.gdfilepath = path(gdfilename).expand()
self.tracknames = sorted(self.tracks.keys())
# Get resource paths instead of filenames
seqfiles = [test_filename(file) for file in seqs]
trackfiles = [test_filename(self.tracks[trackname])
for trackname in self.tracknames]
self.seqfiles = seqfiles
self.trackfiles = trackfiles
tracktuples = [(trackname, trackfile) for trackname, trackfile in
zip(self.tracknames, self.trackfiles)]
load_genomedata(self.gdfilepath, tracktuples, seqfiles,
verbose=self.verbose, mode=self.mode)
if self.mode == "dir":
self.chroms = [val.split(".")[0] for val in seqs]
for chrom in self.chroms:
filename = os.extsep.join([chrom, "genomedata"])
filepath = self.gdfilepath.joinpath(filename)
self.assertTrue(filepath.isfile(),
"Chromosome file was not found: %s" % filepath)
elif self.mode == "file":
self.assertTrue(self.gdfilepath.isfile(),
"Genomedata archive was not created: %r" %
self.gdfilepath)
else:
self.fail("Unrecognized mode: %s" % self.mode)
def setUp(self):
GenomedataTesterBase.setUp(self)
# Create Genomedata collection from test files
seqs = ["chr1.short.fa", "chrY.short.fa.gz"]
# Placental includes data for chr1 and chrY
if self.mode == "dir":
gdfilename = make_temp_dir()
elif self.mode == "file":
tempfile, gdfilename = mkstemp(prefix="genomedata", text=True)
os.close(tempfile)
os.remove(gdfilename) # Allow load_genomedata to create it
else:
self.fail("Unrecognized mode: %s" % self.mode)
self.set_gdfilepath(gdfilename)
self.tracknames = sorted(self.tracks.keys())
# Get resource paths instead of filenames
seqfiles = [test_filename(file) for file in seqs]
trackfiles = [
test_filename(self.tracks[trackname])
for trackname in self.tracknames
]
self.seqfiles = seqfiles
self.trackfiles = trackfiles
tracktuples = [
(trackname, trackfile)
for trackname, trackfile in zip(self.tracknames, self.trackfiles)
]
load_genomedata(self.gdfilepath,
tracktuples,
seqfiles,
verbose=self.verbose,
mode=self.mode)
if self.mode == "dir":
self.chroms = [val.split(".")[0] for val in seqs]
for chrom in self.chroms:
filename = os.extsep.join([chrom, "genomedata"])
filepath = self.gdfilepath.joinpath(filename)
self.assertTrue(filepath.isfile(),
"Chromosome file was not found: %s" % filepath)
elif self.mode == "file":
self.assertTrue(
self.gdfilepath.isfile(),
"Genomedata archive was not created: %r" % self.gdfilepath)
else:
self.fail("Unrecognized mode: %s" % self.mode)
def setUp(self):
# Defaults
self.verbose = False
self.mode = "dir"
# Track to be added by test_add_track
self.new_track = ("primate", "chr1.phyloP44way.primate.short.wigFix")
# Potentially override defaults
self.init() # Call to sub-classed method
# Create Genomedata collection from test files
seqs = ["chr1.short.fa", "chrY.short.fa.gz"]
# Placental includes data for chr1 and chrY
if self.mode == "dir":
gdfilename = make_temp_dir()
elif self.mode == "file":
tempfile, gdfilename = mkstemp(prefix="genomedata")
os.close(tempfile)
os.remove(gdfilename) # Allow load_genomedata to create it
else:
self.fail("Unrecognized mode: %s" % self.mode)
self.gdfilepath = Path(gdfilename).expand()
# Get resource paths instead of filenames
seqfiles = [test_filename(file) for file in seqs]
self.seqfiles = seqfiles
load_genomedata(self.gdfilepath,
None,
seqfiles,
verbose=self.verbose,
mode=self.mode)
if self.mode == "dir":
self.chroms = [val.split(".")[0] for val in seqs]
for chrom in self.chroms:
filename = os.extsep.join([chrom, "genomedata"])
filepath = self.gdfilepath.joinpath(filename)
self.assertTrue(filepath.isfile(),
"Chromosome file was not found: %s" % filepath)
elif self.mode == "file":
self.assertTrue(
self.gdfilepath.isfile(),
"Genomedata archive was not created: %r" % self.gdfilepath)
else:
self.fail("Unrecognized mode: %s" % self.mode)
def setUp(self):
GenomedataTesterBase.setUp(self)
# Create Genomedata collection from test files
seqs = ["chr1.short.fa", "chrY.short.fa.gz"]
# Placental includes data for chr1 and chrY
if self.mode == "dir":
gdfilename = make_temp_dir()
elif self.mode == "file":
tempfile, gdfilename = mkstemp(prefix="genomedata")
os.close(tempfile)
os.remove(gdfilename) # Allow load_genomedata to create it
else:
self.fail("Unrecognized mode: %s" % self.mode)
self.set_gdfilepath(gdfilename)
self.tracknames = sorted(self.tracks.keys())
# Get resource paths instead of filenames
seqfiles = [test_filename(file) for file in seqs]
trackfiles = [test_filename(self.tracks[trackname])
for trackname in self.tracknames]
self.seqfiles = seqfiles
self.trackfiles = trackfiles
tracktuples = [(trackname, trackfile) for trackname, trackfile in
zip(self.tracknames, self.trackfiles)]
load_genomedata(self.gdfilepath, tracktuples, seqfiles,
verbose=self.verbose, mode=self.mode)
if self.mode == "dir":
self.chroms = [val.split(".")[0] for val in seqs]
for chrom in self.chroms:
filename = os.extsep.join([chrom, "genomedata"])
filepath = self.gdfilepath.joinpath(filename)
self.assertTrue(filepath.isfile(),
"Chromosome file was not found: %s" % filepath)
elif self.mode == "file":
self.assertTrue(self.gdfilepath.isfile(),
"Genomedata archive was not created: %r" %
self.gdfilepath)
else:
self.fail("Unrecognized mode: %s" % self.mode)
